Trying to make a spine-like structure in blender
I would do it like this:
- Create the first vertebra
- Shift D Z to duplicate and move upward
- Shift R to repeat the last operation
- S for scaling the needed
- at the end select all the vertebrae and ctrl J Join them
- add a curve modifier to adjust the shape of the whole object


Then create a single bone
in edit mode extrude the bone moving the tip toward the top of the next vertebra
extrude again ...
at the end parent the object to the armature using automatic wheight


I think it can take half an hour for 50-60 pieces

Maybe for 5000 you would need an automated way

Remember also that a long bone can be subdivided n times,  with the W key menu.